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SF1 splicing factor 1 [ Homo sapiens (human) ]

Gene ID: 7536, updated on 7-Apr-2024

Summary

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Official Symbol
SF1provided by HGNC
Official Full Name
splicing factor 1provided by HGNC
Primary source
HGNC:HGNC:12950
See related
Ensembl:ENSG00000168066 MIM:601516; AllianceGenome:HGNC:12950
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BBP; MBBP; ZFM1; ZNF162; D11S636; ZCCHC25
Summary
This gene encodes a nuclear pre-mRNA splicing factor. The encoded protein specifically recognizes the intron branch point sequence at the 3' splice site, together with the large subunit of U2 auxiliary factor (U2AF), and is required for the early stages of spliceosome assembly. It also plays a role in nuclear pre-mRNA retention and transcriptional repression. The encoded protein contains an N-terminal U2AF ligand motif, a central hnRNP K homology motif and quaking 2 region which bind a key branch-site adenosine within the branch point sequence, a zinc knuckles domain, and a C-terminal proline-rich domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
Annotation information
Note: SF1 (Gene ID: 7536) and NR5A1 (Gene ID: 2516) share the SF1 symbol/alias in common. SF1 is a widely used alternative name for nuclear receptor subfamily 5 group A member 1 (NR5A1), which can be confused with the official symbol for SF1 (splicing factor 1). [01 Jun 2018]
Expression
Ubiquitous expression in bone marrow (RPKM 62.1), testis (RPKM 36.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64764606..64778542, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64757911..64771848, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64532078..64546014, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RAS guanyl releasing protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64506559-64507108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64520964-64521574 Neighboring gene glycogen phosphorylase, muscle associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64525447-64526151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526152-64526855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526856-64527560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64527561-64528263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64530587-64531460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64532334-64533208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64533209-64534081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64534082-64534955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:64545791-64546392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64557481-64557982 Neighboring gene mitogen-activated protein kinase kinase kinase kinase 2 Neighboring gene Sharpr-MPRA regulatory region 11124 Neighboring gene MPRA-validated peak1298 silencer Neighboring gene Sharpr-MPRA regulatory region 2965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3491 Neighboring gene menin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1. Nameki N, et al. Protein Sci, 2022 Oct. PMID 36173164, Free PMC Article
  2. SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA. Chatrikhi R, et al. Biophys J, 2016 Dec 20. PMID 28002734, Free PMC Article
  3. Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction. Lin JR, et al. Proteins, 2014 Oct. PMID 25043850
  4. Zinc finger motif-1 antagonizes PDGF-BB-induced growth and dedifferentiation of vascular smooth muscle cells. Cattaruzza M, et al. FASEB J, 2012 Dec. PMID 22906951
  5. Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1. Gupta A, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2011 Apr 1. PMID 21505248, Free PMC Article

See all (160) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.
    Title: Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.
  2. Deoxynivalenol globally affects the selection of 3' splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1.
    Title: Deoxynivalenol globally affects the selection of 3' splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1.
  3. SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA
    Title: SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA.
  4. A novel function of SF1 in the initial recruitment of the U2 snRNP through direct interactions with two U2 snRNP-associated proteins.
    Title: Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins.
  5. Data suggest that post-translational processing of SF1 (phosphorylation of Ser20) down-regulates nuclear import of SF1 via alterations in kinetic interaction of SF1 nuclear localization signal (NLS) with NLS receptor isoforms.
    Title: Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.
  6. We demonstrated that PRPF40B interacts directly with SF1 and associates with U2AF(65
    Title: Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo.
  7. Gomafu indirectly modulates the function of the splicing factors SF1 and Celf3 by sequestering these proteins into separate nuclear bodies.
    Title: Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1.
  8. The conserved SPSP motif phosphorylation and the SF1/U2AF interface are essential in vivo.
    Title: Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex.
  9. Findings suggest that Zinc finger motif-1 (ZFM1) is an important factor for the stabilization of a contractile SMC phenotype under basal or mildly activating conditions.
    Title: Zinc finger motif-1 antagonizes PDGF-BB-induced growth and dedifferentiation of vascular smooth muscle cells.
  10. central ;mystery' domain of SF1 crystals belonged to space group C2 and have most probable solvent contents of 64, 52 or 39% with three, four or five molecules per asymmetric unit, respectively
    Title: Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1.
Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
capsid gag The interaction of HIV-1 CA with human cellular splicing factor 1 (SF1) is identified by yeast two-hybrid screen PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity TAS
Traceable Author Statement
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Leydig cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA 3'-splice site recognition TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in male sex determination IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear body organization IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of steroid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in spliceosomal complex assembly NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of U2AF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nuclear body IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
located_in ribosome NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
splicing factor 1
Names
branch point-binding protein
mammalian branch point-binding protein
transcription factor ZFM1
zinc finger gene in MEN1 locus
zinc finger protein 162

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021399.1 RefSeqGene

    Range
    5001..19241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_617

mRNA and Protein(s)

  1. NM_001178030.2 → NP_001171501.1  splicing factor 1 isoform 6

    See identical proteins and their annotated locations for NP_001171501.1

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS53661.1
    UniProtKB/Swiss-Prot
    Q15637
    Related
    ENSP00000366604.1, ENST00000377387.5
    Conserved Domains (2) summary
    smart00343
    Location:403 → 418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142 → 382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  2. NM_001178031.3 → NP_001171502.1  splicing factor 1 isoform 5

    See identical proteins and their annotated locations for NP_001171502.1

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC000773, DC317188, DC341853
    Consensus CDS
    CCDS53660.1
    UniProtKB/TrEMBL
    B4DJU4
    Related
    ENSP00000396793.2, ENST00000433274.6
    Conserved Domains (2) summary
    smart00343
    Location:252 → 267
    ZnF_C2HC; zinc finger
    COG5176
    Location:10 → 231
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  3. NM_001346363.2 → NP_001333292.1  splicing factor 1 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC000773, BC020217, BE745705, DC341853
    UniProtKB/TrEMBL
    A0A9L9PXR5, H7C561
    Related
    ENSP00000419062.2, ENST00000486867.2
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  4. NM_001346364.2 → NP_001333293.1  splicing factor 1 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC020217, BC069273, BE745705, DC341853
    UniProtKB/TrEMBL
    A0A9L9PXR5
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  5. NM_001346409.2 → NP_001333338.1  splicing factor 1 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AK301803, AP001462, BC069273
    UniProtKB/TrEMBL
    B4DSE4, B4DX42, E7ESU3
    Conserved Domains (2) summary
    smart00343
    Location:163 → 178
    ZnF_C2HC; zinc finger
    cd22382
    Location:20 → 112
    KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins

  6. NM_001346410.2 → NP_001333339.1  splicing factor 1 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP001462, BC032676, BC069273
    Conserved Domains (2) summary
    smart00343
    Location:163 → 178
    ZnF_C2HC; zinc finger
    cd22382
    Location:20 → 112
    KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins

  7. NM_001378956.1 → NP_001365885.1  splicing factor 1 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP001462
    UniProtKB/TrEMBL
    A0A9L9PXE4
    Related
    ENSP00000516498.1, ENST00000706684.1
    Conserved Domains (2) summary
    smart00343
    Location:403 → 418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142 → 382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  8. NM_001378957.1 → NP_001365886.1  splicing factor 1 isoform 12

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS91502.1
    UniProtKB/TrEMBL
    A0A7P0T9U7, B4DJU4
    Related
    ENSP00000505779.1, ENST00000681407.1
    Conserved Domains (2) summary
    smart00343
    Location:403 → 418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142 → 382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  9. NM_004630.4 → NP_004621.2  splicing factor 1 isoform 1

    See identical proteins and their annotated locations for NP_004621.2

    Status: REVIEWED

    Source sequence(s)
    BC069273, DC368015, DC370979, Y08765
    Consensus CDS
    CCDS31599.1
    UniProtKB/Swiss-Prot
    B7Z1Q1, C9JJE2, Q14818, Q14819, Q15637, Q15913, Q8IY00, Q92744, Q92745, Q969H7, Q9BW01, Q9UEI0
    UniProtKB/TrEMBL
    B4DJU4
    Related
    ENSP00000366607.3, ENST00000377390.8
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  10. NM_201995.3 → NP_973724.1  splicing factor 1 isoform 2

    See identical proteins and their annotated locations for NP_973724.1

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS8080.1
    UniProtKB/TrEMBL
    B4DJU4
    Related
    ENSP00000334414.5, ENST00000334944.9
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  11. NM_201997.3 → NP_973726.2  splicing factor 1 isoform 4

    See identical proteins and their annotated locations for NP_973726.2

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS44642.2
    UniProtKB/TrEMBL
    A0A9L9PXR5
    Related
    ENSP00000366611.3, ENST00000377394.7
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

  12. NM_201998.3 → NP_973727.1  splicing factor 1 isoform 3

    See identical proteins and their annotated locations for NP_973727.1

    Status: REVIEWED

    Source sequence(s)
    BC020217, BC069273
    Consensus CDS
    CCDS8081.1
    UniProtKB/TrEMBL
    B4DSE4
    Related
    ENSP00000227503.9, ENST00000227503.13
    Conserved Domains (2) summary
    smart00343
    Location:278 → 293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17 → 257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    64764606..64778542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427551.1 → XP_047283507.1  splicing factor 1 isoform X6

  2. XM_047427550.1 → XP_047283506.1  splicing factor 1 isoform X5

  3. XM_017018246.2 → XP_016873735.2  splicing factor 1 isoform X2

  4. XM_047427549.1 → XP_047283505.1  splicing factor 1 isoform X1

  5. XM_011545248.2 → XP_011543550.2  splicing factor 1 isoform X4

  6. XM_011545247.2 → XP_011543549.2  splicing factor 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64757911..64771848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369869.1 → XP_054225844.1  splicing factor 1 isoform X6

  2. XM_054369868.1 → XP_054225843.1  splicing factor 1 isoform X5

  3. XM_054369865.1 → XP_054225840.1  splicing factor 1 isoform X2

  4. XM_054369864.1 → XP_054225839.1  splicing factor 1 isoform X1

  5. XM_054369867.1 → XP_054225842.1  splicing factor 1 isoform X4

  6. XM_054369866.1 → XP_054225841.1  splicing factor 1 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_033649.1: Suppressed sequence

    Description
    NR_033649.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.

  2. NR_033650.1: Suppressed sequence

    Description
    NR_033650.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15637.4 GenPept UniProtKB/Swiss-Prot:Q15637

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